Quality Control

1. Porechop was run to trim adapter sequences from reads and discard reads with adapters found in the middle. More detailed information can be found in porechop_log. For quality control plots of the reads after this step, see plot_pre.
2. Reads were aligned to the TB reference NC_000962.3.fa using Minimap2.
3. All reads which did not map to NC_000962.3.fa were removed. Prior to filtering there were 143591 reads. After filtering there remains 142032. This means 98.91% of reads mapped to NC_000962.3.fa. For more stats on the pre-filtered reads see stats_pre and for post-filtered reads see stats_post. For quality control plots of the reads after this step (and read percent identity to NC_000962.3.fa) see plot_post. Stats were produced with NanoStat and plots with Pistis.

Mykrobe Analysis

Phylogenetic group: Mycobacterium_tuberculosis_complex

Species: Mycobacterium_tuberculosis

Lineage: Beijing_East_Asia

A summary of the susceptiblity information from Mykrobe predict is shown here. For the full report, see mykrobe. If resistance is identified for a drug then the predicted responsible variant(s) is given, along with supporting information.

• Rifampicin

  • Prediction: Susceptible

• Quinolones

  • Prediction: Resistant
  • Called by: gyrA_A90V-A90V
  • Reference median depth: 0
  • Alternate median depth: 14

• Ethambutol

  • Prediction: Resistant
  • Called by: embB_Q497R-Q497R
  • Reference median depth: 0
  • Alternate median depth: 7

• Isoniazid

  • Prediction: Resistant
  • Called by: katG_S315T-S315T
  • Reference median depth: 0
  • Alternate median depth: 15

• Capreomycin

  • Prediction: Susceptible

• Amikacin

  • Prediction: Susceptible

• Streptomycin

  • Prediction: Resistant
  • Called by: rpsL_K43R-K43R
  • Reference median depth: 0
  • Alternate median depth: 7

• Pyrazinamide

  • Prediction: Susceptible

• Kanamycin

  • Prediction: Resistant
  • Called by: eis_G-10A-G
  • Reference median depth: 0
  • Alternate median depth: 7